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Consider explode() [php.net] or serialize() [php.net] to set one cookie with multiple names and values
If you need to track that many vars I would consider using Sessions [php.net]
I've tried to do it with explode and set all values in 1 big cookie, but seems it's just too difficult for me, i just can't get it to work properly.
I did found a workaround, thanks to your advice:
I let the php file in the subdirectory redirect to the root, where the cookies are set, and let the root redirect back to the subdirectory. And it works ok, thanks again.